Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008259.1 Hibiscus syriacus cultivar Beakdansim tig00110912_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2373650
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 11
Found at i:511127 original size:2 final size:2
Alignment explanation
Indices: 511109--511538 Score: 129
Period size: 2 Copynumber: 234.5 Consensus size: 2
511099 TAATATAAAA
* *
511109 AT AT A- AT AT AT AA AT AT AT AT -T AT GAT AT AC AT A- AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
* *
511148 AT AT A- AT ACC AT AT A- AT ACC AT AT A- AT A- AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * * * *
511188 AC AT AT -T GT AT ACT GT AA AT AT AC A- AT AT A- AT ACT AT AT A-
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
511228 AT A- AT A- AT A- AT AT AT A- AT AT AT AT A- AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
511264 AA AT AT AT AT -T AT A- AT ACT AT AT A- AT A- AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * *
511302 A- AA AT TT TT ACT AT AT A- AT AT A- AT AT A- AT A- AT AT AT A-
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
511339 AT AC AT A- AT AT AT A- AT AT AT A- AT AT A- AC A- AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
511375 TT AT A- AT AT AA AGT AT AT -T ACT ACT AT AT A- AT AT A- AGG CT
1 AT AT AT AT AT AT A-T AT AT AT A-T A-T AT AT AT AT AT AT A-T AT
* *
511415 A- AT AT AT AT AT ACT AT AT A- AT AT A- AT CT TT A- AT AT AT A-
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
511453 AC AT GT AT AT A- AT AT A- AT AT -T AT AT A- AT AT AT -T AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
511489 AT AT AT AT A- AT AT AT AT -T GT AC ACT AT AT AT ACT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT
*
511530 GT AT AT AT A
1 AT AT AT AT A
511539 AAAGGTCGGA
Statistics
Matches: 321, Mismatches: 41, Indels: 132
0.65 0.08 0.27
Matches are distributed among these distances:
1 53 0.17
2 246 0.77
3 22 0.07
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:511233 original size:13 final size:13
Alignment explanation
Indices: 511160--511293 Score: 77
Period size: 13 Copynumber: 11.5 Consensus size: 13
511150 ATAATACCAT
*
511160 ATAATACCATATA
1 ATAATACTATATA
511173 ATAATA-TATAT-
1 ATAATACTATATA
*
511184 AT-ATAC-ATATT
1 ATAATACTATATA
* *
511195 GT-ATACTGTA-A
1 ATAATACTATATA
511206 AT-ATAC-A-AT-
1 ATAATACTATATA
511215 ATAATACTATATA
1 ATAATACTATATA
*
511228 ATAATAATA-ATA
1 ATAATACTATATA
511240 TATAATA-TATATA
1 -ATAATACTATATA
511253 AT-ATA-TA-AT-
1 ATAATACTATATA
*
511262 ATAAATA-TATATT
1 AT-AATACTATATA
511275 ATAATACTATATA
1 ATAATACTATATA
511288 ATAATA
1 ATAATA
511294 TAATATATAA
Statistics
Matches: 98, Mismatches: 8, Indels: 30
0.72 0.06 0.22
Matches are distributed among these distances:
9 5 0.05
10 13 0.13
11 23 0.23
12 21 0.21
13 36 0.37
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (13 bp):
ATAATACTATATA
Found at i:519727 original size:20 final size:21
Alignment explanation
Indices: 519688--519727 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
519678 CCCCCTTTGA
*
519688 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATTACCCCCAC
*
519709 AGGGGAATCGA-TACCCCCA
1 AGGGGAACCGATTACCCCCA
519728 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.38, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATTACCCCCAC
Found at i:529839 original size:2 final size:2
Alignment explanation
Indices: 529822--529854 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
529812 ATATTATAAC
*
529822 TA TA TT TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
529855 AAGATTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:533749 original size:33 final size:33
Alignment explanation
Indices: 533662--533752 Score: 155
Period size: 33 Copynumber: 2.8 Consensus size: 33
533652 GATACAGTGG
* *
533662 TTCGATTGCTTACTATTTATTATAAATTTTCCT
1 TTCGATTGCTTATTATTTATTTTAAATTTTCCT
*
533695 TTCGATCGCTTATTATTTATTTTAAATTTTCCT
1 TTCGATTGCTTATTATTTATTTTAAATTTTCCT
533728 TTCGATTGCTTATTATTTATTTTAA
1 TTCGATTGCTTATTATTTATTTTAA
533753 TTTGTCCAGT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.23, C:0.13, G:0.07, T:0.57
Consensus pattern (33 bp):
TTCGATTGCTTATTATTTATTTTAAATTTTCCT
Found at i:537135 original size:22 final size:22
Alignment explanation
Indices: 537107--537157 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
537097 CTTACCGCAT
537107 GTCCTTATGCTATAAGTATAAG
1 GTCCTTATGCTATAAGTATAAG
537129 GTCCTTATGCTATAAGTATAAG
1 GTCCTTATGCTATAAGTATAAG
537151 GTCCTTA
1 GTCCTTA
537158 CTAGGTGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (22 bp):
GTCCTTATGCTATAAGTATAAG
Found at i:540149 original size:17 final size:17
Alignment explanation
Indices: 540095--540149 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
540085 TCGGTCAACT
*
540095 GTTGACCGTTGACTGACC
1 GTTGACCATTGACTGA-C
* *
540113 GTTGACCTTTGA-TCGGC
1 GTTGACCATTGACT-GAC
540130 GTTGACCATTGACTGAC
1 GTTGACCATTGACTGAC
540147 GTT
1 GTT
540150 AACTTTTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 18 0.58
18 13 0.42
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (17 bp):
GTTGACCATTGACTGAC
Found at i:541312 original size:18 final size:16
Alignment explanation
Indices: 541270--541312 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 16
541260 ATTAAATATT
*
541270 ATATTTTTAAATTTGA
1 ATATTTTTAAATTTAA
541286 ATATATTTTACAATATTAA
1 ATAT-TTTTA-AAT-TTAA
541305 ATATTTTT
1 ATATTTTT
541313 TTATGGTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 4 0.17
17 5 0.22
18 7 0.30
19 7 0.30
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (16 bp):
ATATTTTTAAATTTAA
Found at i:541521 original size:20 final size:21
Alignment explanation
Indices: 541496--541535 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
541486 CAGCAAAACA
*
541496 AGTCTT-TAGTGACGTTTTTT
1 AGTCTTATAGCGACGTTTTTT
*
541516 AGTCTTATAGCGGCGTTTTT
1 AGTCTTATAGCGACGTTTTT
541536 AAGCGCCGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (21 bp):
AGTCTTATAGCGACGTTTTTT
Found at i:541746 original size:43 final size:43
Alignment explanation
Indices: 541699--541853 Score: 115
Period size: 43 Copynumber: 3.7 Consensus size: 43
541689 CGTTAATTAT
* * * *
541699 CTTGTCTTTAGTAGCCTTTTTTGCGACAAACACCGCTAATTCG
1 CTTGTCTTTAGTGGCATTTTTTGCCACAAACACCACTAATTCG
* * * * * *
541742 CTTG----TAATGGCTTTTTTTTCTACAAACGCCACTAATTCT
1 CTTGTCTTTAGTGGCATTTTTTGCCACAAACACCACTAATTCG
* *
541781 CTTGTCTTTAGTGGCATTTTTTGCCACAAA-ATCTACTAATTCT
1 CTTGTCTTTAGTGGCATTTTTTGCCACAAACA-CCACTAATTCG
* * **
541824 ATTGTTTTTAGTGGCGCTTTTT-CCACAAAC
1 CTTGTCTTTAGTGGCATTTTTTGCCACAAAC
541854 GTTGCTAATT
Statistics
Matches: 88, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
39 31 0.35
42 7 0.08
43 50 0.57
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42
Consensus pattern (43 bp):
CTTGTCTTTAGTGGCATTTTTTGCCACAAACACCACTAATTCG
Found at i:541863 original size:42 final size:42
Alignment explanation
Indices: 541773--541913 Score: 167
Period size: 43 Copynumber: 3.3 Consensus size: 42
541763 ACAAACGCCA
* * *
541773 CTAATTCTCTTGTCTTTAGTGGCATTTTTTGCCACAAAATCTA
1 CTAATTCTATTGTCTTTAGTGGCGTTTTTTGCCACAAAAT-TG
* * *
541816 CTAATTCTATTGTTTTTAGTGGCGCTTTTT-CCACAAACGTTG
1 CTAATTCTATTGTCTTTAGTGGCGTTTTTTGCCACAAA-ATTG
* * *
541858 CTAATTCTATTGTCTTTAGTAGTGTTTTTTGCCATAAAATTCG
1 CTAATTCTATTGTCTTTAGTGGCGTTTTTTGCCACAAAATT-G
541901 CTAATTCTATTGT
1 CTAATTCTATTGT
541914 TTTCAATGAC
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
42 36 0.43
43 47 0.57
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (42 bp):
CTAATTCTATTGTCTTTAGTGGCGTTTTTTGCCACAAAATTG
Found at i:545643 original size:41 final size:41
Alignment explanation
Indices: 545523--545726 Score: 138
Period size: 41 Copynumber: 5.0 Consensus size: 41
545513 CAAAAAAATG
545523 CCACTATAGATGAA-CCTATTGCGGTA-TTTGTATAAAAACA
1 CCACTATAGATGAATCCTATTGCGG-AGTTTGTATAAAAACA
* * * * **
545563 CCGCTAAAG-T-ACTACTTTATT-ATGACGTTTTGT-TGAAAAACA
1 CCACTATAGATGAAT-C-CTATTGCGGA-G-TTTGTAT-AAAAACA
*
545605 CCACTATAGATGAATCCTATTGCGGAGTTTGTATAAAAACG
1 CCACTATAGATGAATCCTATTGCGGAGTTTGTATAAAAACA
* * * * *
545646 CCGCTAAAGTATTACT-CTATTGCGGCGTTTGT-TGAAAAA-A
1 CCACTATAG-ATGAATCCTATTGCGGAGTTTGTAT-AAAAACA
* *
545686 CGCACTATAGATGAACCCTATTGCGGCGTTTGTATAAAAAC
1 C-CACTATAGATGAATCCTATTGCGGAGTTTGTATAAAAAC
545727 GCCGCTAAAG
Statistics
Matches: 123, Mismatches: 24, Indels: 32
0.69 0.13 0.18
Matches are distributed among these distances:
38 1 0.01
39 2 0.02
40 14 0.11
41 70 0.57
42 30 0.24
43 4 0.03
44 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (41 bp):
CCACTATAGATGAATCCTATTGCGGAGTTTGTATAAAAACA
Found at i:545683 original size:82 final size:80
Alignment explanation
Indices: 545465--545737 Score: 334
Period size: 83 Copynumber: 3.3 Consensus size: 80
545455 CTATTATAGC
* * * * *
545465 GTTTGTAAAAAAATGCCGCTATAGTACTACTTTGTTGTGGCGTTAT-TTCAAAAAAATGCCACTA
1 GTTTGTATAAAAACGCCGCTAAAGTACTACTTTATTGTGGCGTT-TGTT-GAAAAAA--CCACTA
545529 TAGATGAACCTATTGCGGTA
62 TAGATGAACCTATTGCGG-A
* * *
545549 -TTTGTATAAAAACACCGCTAAAGTACTACTTTATTATGACGTTTTGTTGAAAAACACCACTATA
1 GTTTGTATAAAAACGCCGCTAAAGTACTACTTTATTGTGGCG-TTTGTTGAAAAA-ACCACTATA
545613 GATGAATCCTATTGCGGA
64 GATGAA-CCTATTGCGGA
* * *
545631 GTTTGTATAAAAACGCCGCTAAAGTATTACTCTATTGCGGCGTTTGTTGAAAAAACGCACTATAG
1 GTTTGTATAAAAACGCCGCTAAAGTACTACTTTATTGTGGCGTTTGTTGAAAAAAC-CACTATAG
*
545696 ATGAACCCTATTGCGGC
65 ATGAA-CCTATTGCGGA
545713 GTTTGTATAAAAACGCCGCTAAAGT
1 GTTTGTATAAAAACGCCGCTAAAGT
545738 TACCATTTTG
Statistics
Matches: 167, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
81 2 0.01
82 75 0.45
83 85 0.51
84 5 0.03
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (80 bp):
GTTTGTATAAAAACGCCGCTAAAGTACTACTTTATTGTGGCGTTTGTTGAAAAAACCACTATAGA
TGAACCTATTGCGGA
Found at i:547451 original size:16 final size:18
Alignment explanation
Indices: 547432--547465 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
547422 AAAACGAATC
547432 AAAAG-ATT-TTGATGTT
1 AAAAGAATTGTTGATGTT
547448 AAAAGAATTGTTGATGTT
1 AAAAGAATTGTTGATGTT
547466 TCTTGAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 3 0.19
18 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (18 bp):
AAAAGAATTGTTGATGTT
Found at i:552379 original size:23 final size:22
Alignment explanation
Indices: 552327--552372 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
552317 AAAAATAAAA
*
552327 ATAAAGAAAAACAAAAAACACTC
1 ATAAA-AAAAACAAAAAAAACTC
552350 ATGAAAAAAAACAAAACAAAACT
1 AT-AAAAAAAACAAAA-AAAACT
552373 TCTAAAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.72, C:0.15, G:0.04, T:0.09
Consensus pattern (22 bp):
ATAAAAAAAACAAAAAAAACTC
Found at i:555530 original size:24 final size:24
Alignment explanation
Indices: 555503--555552 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
555493 ATAAAGAACC
555503 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
555527 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
555551 AA
1 AA
555553 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:559120 original size:31 final size:31
Alignment explanation
Indices: 559059--559120 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
559049 TATTGTTATG
*
559059 TTATAATTTTTTGATATATTTATAATATTAA
1 TTATAATTTTTTGATATATTTATAAAATTAA
559090 TTATAA-TTTTTG-TAATATTTATAAAAATTAA
1 TTATAATTTTTTGAT-ATATTTAT-AAAATTAA
559121 AATGTGACCG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 1 0.04
30 14 0.50
31 13 0.46
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (31 bp):
TTATAATTTTTTGATATATTTATAAAATTAA
Found at i:560434 original size:19 final size:19
Alignment explanation
Indices: 560392--560443 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
560382 TTTAAAGATT
* *
560392 TAAAATTTATAAAATTATAT
1 TAAAATTTAT-AAATAATAA
560412 TAAAATTTATAAATAATAA
1 TAAAATTTATAAATAATAA
560431 T-AAATATTATAAA
1 TAAAAT-TTATAAA
560444 CTTGAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 4 0.14
19 15 0.52
20 10 0.34
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAATTTATAAATAATAA
Found at i:562217 original size:194 final size:194
Alignment explanation
Indices: 561929--562362 Score: 566
Period size: 194 Copynumber: 2.2 Consensus size: 194
561919 ATTGAAATTT
* * * * * * **
561929 GTATCGATACTTTTCTAAATATATGCACCAAATTATTGATACTTTAGGAATTTTAAAAAATTGTA
1 GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTTAAAAAATTACA
* * * * * *
561994 ATAATAGTGCATATAAAGTATCGATACTTTATAAACATGTATCGATACATAACAATATTACAGGT
66 ATAATAGCGCATATAAAGTATCCATACTTTAGAAACATGTATCAATACATAACAATATAACAAGT
* * *
562059 AAAAATATGA-AAAAGTCGGTTTCAATATGACAAAACCGGTAAAGAGCAACCGGATATGTTGAAG
131 AAAAATACGACAAAA-CCAGTTTCAATATGACAAAACCGGTAAAGAGCAACCGGATATGTTGAAG
* * *
562123 GTATCGATACTTTTATAAGTATATATATCATACTATCGATACTTTATGAA-TTTAAAAGAATTAC
1 GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTTAAAA-AATTAC
* * * *
562187 AATAGTAGCGCCTATAAAGTATCCATACTTTAGAAATATGTATCAATACATGACAATATAACAAG
65 AATAATAGCGCATATAAAGTATCCATACTTTAGAAACATGTATCAATACATAACAATATAACAAG
* * * *
562252 TTAAAATACGACAAAACCAGTTTCAATATGACAAAACCGGTAAAGCGCTATCGGATATGTTGAAG
130 TAAAAATACGACAAAACCAGTTTCAATATGACAAAACCGGTAAAGAGCAACCGGATATGTTGAAG
* *
562317 GTATCGATACTTTAATAAGTGTATGTATCATATTATCGATACTTTA
1 GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTA
562363 AAAAGAAAAA
Statistics
Matches: 206, Mismatches: 32, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
193 7 0.03
194 195 0.95
195 4 0.02
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (194 bp):
GTATCGATACTTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTTAAAAAATTACA
ATAATAGCGCATATAAAGTATCCATACTTTAGAAACATGTATCAATACATAACAATATAACAAGT
AAAAATACGACAAAACCAGTTTCAATATGACAAAACCGGTAAAGAGCAACCGGATATGTTGAAG
Found at i:563015 original size:19 final size:19
Alignment explanation
Indices: 562957--563025 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
562947 TTATAAAGTG
562957 ATATTATAGGTAGAAAATAA
1 ATATTATAGGTAGAAAAT-A
* * * *
562977 ATATTGATA-CTTGTATATA
1 ATATT-ATAGGTAGAAAATA
562996 ATATTATAGGTAGAAAATA
1 ATATTATAGGTAGAAAATA
*
563015 ATATTGTAGGT
1 ATATTATAGGT
563026 TATATAAATG
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
18 3 0.08
19 22 0.58
20 10 0.26
21 3 0.08
ACGTcount: A:0.45, C:0.01, G:0.16, T:0.38
Consensus pattern (19 bp):
ATATTATAGGTAGAAAATA
Found at i:563076 original size:230 final size:230
Alignment explanation
Indices: 562666--563081 Score: 699
Period size: 230 Copynumber: 1.8 Consensus size: 230
562656 AAATAGGGGT
*
562666 TTTATGGGTTTGGGGGTTTCAAAGCAAAGAAGGATTTCAGACCGATTAGAGTTAGAAAGTGATAT
1 TTTATGGGTTTGGGGATTTCAAAGCAAAGAAGGATTTCAGACCGATTAGAGTTAGAAAGTGATAT
*
562731 TATAGGTAGAAAATAAATATCGATACTTGTATATAATATTATAGGTAGAAAATGATATTGTAGGT
66 TATAGGTAGAAAATAAATATCGATACTTGTATATAATATTATAGGTAGAAAATAATATTGTAGGT
* *
562796 TGTATAAATGTACTGATACTTGTAGTAGAGAGTATTCCCATTCGTTTGAAGGAAACCCTAGTTTT
131 TATATAAATGTACTGATACTTGTAATAGAGAGTATTCCCATTCGTTTGAAGGAAACCCTAGTTTT
562861 TTTAGTATTATAGTAATCAGAAATAGGGATTAGGG
196 TTTAGTATTATAGTAATCAGAAATAGGGATTAGGG
** ** *
562896 TTTATGGGTTTGGGGATTTTGAAGCAAAGAAGGATTTGGGACCGATTAGAGTTATAAAGTGATAT
1 TTTATGGGTTTGGGGATTTCAAAGCAAAGAAGGATTTCAGACCGATTAGAGTTAGAAAGTGATAT
*
562961 TATAGGTAGAAAATAAATATTGATACTTGTATATAATATTATAGGTAGAAAATAATATTGTAGGT
66 TATAGGTAGAAAATAAATATCGATACTTGTATATAATATTATAGGTAGAAAATAATATTGTAGGT
** *
563026 TATATAAATGTATCT-ATACTTGTAATAGAGAGTATTCTGATTCTTTTGAAGGAAAC
131 TATATAAATGTA-CTGATACTTGTAATAGAGAGTATTCCCATTCGTTTGAAGGAAAC
563082 TGTTTTACTA
Statistics
Matches: 172, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
230 170 0.99
231 2 0.01
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.35
Consensus pattern (230 bp):
TTTATGGGTTTGGGGATTTCAAAGCAAAGAAGGATTTCAGACCGATTAGAGTTAGAAAGTGATAT
TATAGGTAGAAAATAAATATCGATACTTGTATATAATATTATAGGTAGAAAATAATATTGTAGGT
TATATAAATGTACTGATACTTGTAATAGAGAGTATTCCCATTCGTTTGAAGGAAACCCTAGTTTT
TTTAGTATTATAGTAATCAGAAATAGGGATTAGGG
Found at i:566153 original size:13 final size:13
Alignment explanation
Indices: 566135--566196 Score: 70
Period size: 13 Copynumber: 4.8 Consensus size: 13
566125 TGCGTCATAA
*
566135 ATTTATGACGCGC
1 ATTTATGACGCAC
* *
566148 ATTTATGGCACAC
1 ATTTATGACGCAC
*
566161 ATTTATGACACAC
1 ATTTATGACGCAC
* *
566174 ATTTATGATGCGC
1 ATTTATGACGCAC
566187 ATTTATGACG
1 ATTTATGACG
566197 TTCATTGAGC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (13 bp):
ATTTATGACGCAC
Found at i:566273 original size:85 final size:85
Alignment explanation
Indices: 566174--566339 Score: 205
Period size: 85 Copynumber: 2.0 Consensus size: 85
566164 TATGACACAC
** * *
566174 ATTTATGATGCGCATTTATGACGTT-CATTGAGCGTCATTGAAGC-C-C-CCATCATAAATTAAG
1 ATTTATGACACGCATGTATGAC-TTACATTGAGCGTCATTGAAGCACACGCCAT--TAAA-AAAG
*
566235 ATGACACACATTTGTGTGTCATAA
62 ATGACACACATTCGTGTGTCATAA
* *
566259 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCACACGCCATTAAAAAAGATGA
1 ATTTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCACACGCCATTAAAAAAGATGA
566324 CACACATTCGTGTGTC
66 CACACATTCGTGTGTC
566340 GTGATTGTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
84 2 0.03
85 58 0.83
86 5 0.07
87 1 0.01
88 4 0.06
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCACACGCCATTAAAAAAGATGA
CACACATTCGTGTGTCATAA
Found at i:566372 original size:2 final size:2
Alignment explanation
Indices: 566365--566396 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
566355 AAATTATTGT
566365 TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
566397 GATTGACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:569388 original size:21 final size:21
Alignment explanation
Indices: 569342--569388 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
569332 GTAAACATGA
**
569342 AGTATCGATACTTTTTGTATT
1 AGTATCGATACTTTTTGTACC
*
569363 TGTATCGATACTTTTTTGT-CC
1 AGTATCGATAC-TTTTTGTACC
569384 AGTAT
1 AGTAT
569389 GTTTTCCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.51
Consensus pattern (21 bp):
AGTATCGATACTTTTTGTACC
Found at i:569675 original size:200 final size:200
Alignment explanation
Indices: 569062--569789 Score: 974
Period size: 200 Copynumber: 3.7 Consensus size: 200
569052 TGCATTTCAT
* * *
569062 CTTCGAAACCGATTAGTATAAAGTAATAGGTAAATTT--AA---AA-T-GT---AATATACCAGT
1 CTTCAAAACCGATTAATATAAAGTAATAGGTAAATTTACAATGTAAGTGGTAAAAATATACCGGT
* * *
569117 TTAATGACAAGATACGTAAACATAAAGTATCGATACTTTTTGTATGTGTATCGATACTTTTTGTC
66 TTAATGACAAAATACGTAAACACAAAGTATCAATACTTTTTGTATGTGTATCGATACTTTTTGTC
* * * * * * * * *
569182 TAGTATGCATCCCAAACGAGATACACACATAAAGTATCGATACACTTATGTA-AAGTATCGATTC
131 CAGTATGCTTTCCAAACTAGATGCACGCAGAAAGTATCGATACACGTACG-AGAAGTATCGATTC
569246 TTAAAA
195 TTAAAA
* * * * * * *
569252 CTTCAAAACCAATTAATTTAAGGTAATAGCTAAATTTACAAGGTTAGAGGTAAAAATATACCGGT
1 CTTCAAAACCGATTAATATAAAGTAATAGGTAAATTTACAATGTAAGTGGTAAAAATATACCGGT
* ** * *
569317 TTAAAGACAAAATACGTAAACATGAAGTATCGATACTTTTTGTATTTGTATCGATACTTTTTTGT
66 TTAATGACAAAATACGTAAACACAAAGTATCAATACTTTTTGTATGTGTATCGATAC-TTTTTGT
*
569382 CCAGTATGTTTTCCAAACTAGATGCACGCAGAAAGTATCGATACACGTACGAGAAGTATCGATTC
130 CCAGTATGCTTTCCAAACTAGATGCACGCAGAAAGTATCGATACACGTACGAGAAGTATCGATTC
569447 TTAAAA
195 TTAAAA
*
569453 CTTCAAAACTGATTAATATAAAGTAATAGGTAAATTTACAATGTAAGTGGTAAAAATATACCGGT
1 CTTCAAAACCGATTAATATAAAGTAATAGGTAAATTTACAATGTAAGTGGTAAAAATATACCGGT
* * *
569518 TTAGTGAAAAAATATGTAAACACAAAGTATCAATACTTTTTGTATGTGTATCGATACTTTTTGTC
66 TTAATGACAAAATACGTAAACACAAAGTATCAATACTTTTTGTATGTGTATCGATACTTTTTGTC
* * *
569583 CAGTATGCTTTCCAAACTAGATGCATGTAGAAAGTATCGATACACGTACGAGAGGTATCGATTCT
131 CAGTATGCTTTCCAAACTAGATGCACGCAGAAAGTATCGATACACGTACGAGAAGTATCGATTCT
569648 TAAAA
196 TAAAA
* * * * **
569653 ATTCAAAACCGATTAGTATAAAGTAATAAGTAAATTTACAATGTAAGCGGTAAAAATATACATGT
1 CTTCAAAACCGATTAATATAAAGTAATAGGTAAATTTACAATGTAAGTGGTAAAAATATACCGGT
* *
569718 TTAATGACAAAATACGTAAACACAAAGTATCAATATTTTTTGTATGTGTATTGATACTTTTTGTC
66 TTAATGACAAAATACGTAAACACAAAGTATCAATACTTTTTGTATGTGTATCGATACTTTTTGTC
569783 CAGTATG
131 CAGTATG
569790 AAAACACCGA
Statistics
Matches: 471, Mismatches: 55, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
190 31 0.07
192 2 0.00
195 1 0.00
197 2 0.00
200 263 0.56
201 172 0.37
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (200 bp):
CTTCAAAACCGATTAATATAAAGTAATAGGTAAATTTACAATGTAAGTGGTAAAAATATACCGGT
TTAATGACAAAATACGTAAACACAAAGTATCAATACTTTTTGTATGTGTATCGATACTTTTTGTC
CAGTATGCTTTCCAAACTAGATGCACGCAGAAAGTATCGATACACGTACGAGAAGTATCGATTCT
TAAAA
Found at i:572579 original size:15 final size:15
Alignment explanation
Indices: 572559--572588 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
572549 AAGAGAAGAA
572559 AACATTGTTATGTAT
1 AACATTGTTATGTAT
*
572574 AACATTGTTTTGTAT
1 AACATTGTTATGTAT
572589 GTATGTTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (15 bp):
AACATTGTTATGTAT
Found at i:572850 original size:6 final size:6
Alignment explanation
Indices: 572839--572974 Score: 94
Period size: 6 Copynumber: 22.7 Consensus size: 6
572829 TTTATGCAGT
* * * *
572839 TTTCAA TTTCAA TTTCAGA -CTGAA TTTCAT TTTCAA TTTCAA TTTTAA
1 TTTCAA TTTCAA TTTCA-A TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
*** * * * * *
572887 TTTGTG TTTCAA TTTTAA TATCAA TTTTAA TTTGAG TTTCAA TTTCAA
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
* * * * * *
572935 TATCAA TTTTAA TTTGAG TTTGAA TTTTAA TTTCAA TTTC
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTC
572975 GGCCCCACTA
Statistics
Matches: 98, Mismatches: 30, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
5 1 0.01
6 96 0.98
7 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (6 bp):
TTTCAA
Found at i:572897 original size:30 final size:29
Alignment explanation
Indices: 572863--572973 Score: 141
Period size: 30 Copynumber: 3.7 Consensus size: 29
572853 TCAGACTGAA
* *
572863 TTTCATTTTCAATTTCAATTTTAATTTGTG
1 TTTCATTTT-AATATCAATTTTAATTTGAG
572893 TTTCAATTTTAATATCAATTTTAATTTGAG
1 TTTC-ATTTTAATATCAATTTTAATTTGAG
*
572923 TTTCAATTTCAATATCAATTTTAATTTGAG
1 TTTC-ATTTTAATATCAATTTTAATTTGAG
* *
572953 TTTGAATTTTAATTTCAATTT
1 TTT-CATTTTAATATCAATTT
572974 CGGCCCCACT
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
30 68 0.93
31 5 0.07
ACGTcount: A:0.30, C:0.08, G:0.06, T:0.56
Consensus pattern (29 bp):
TTTCATTTTAATATCAATTTTAATTTGAG
Found at i:575072 original size:22 final size:22
Alignment explanation
Indices: 575033--575077 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
575023 ATTATGCCAG
* ** *
575033 TTTGATTAAAAGGTTAAATGCC
1 TTTGAGTAAAAGACTAAAAGCC
575055 TTTGAGTAAAAGACTAAAAGCC
1 TTTGAGTAAAAGACTAAAAGCC
575077 T
1 T
575078 AGATGTGCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (22 bp):
TTTGAGTAAAAGACTAAAAGCC
Found at i:575078 original size:82 final size:81
Alignment explanation
Indices: 574817--575132 Score: 402
Period size: 81 Copynumber: 3.9 Consensus size: 81
574807 ACTGTTCTAA
* * * *
574817 AGTAAAAGACTAAAAGCCTAGCTGCGCATTTGACAAAAAGGTGT--ATTATCCCAGTTAGATGAA
1 AGTAAAAGACTAAAAGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
574880 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* ** * * * * *
574896 AGTAAAAGATTAATGGCCTAGTTGTGCATTTGATATAAAGGTGTCAATGATGTCAGTTAGATGAA
1 AGTAAAAGACTAAAAGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
574961 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* ** * *
574977 AGTAAAAGATTAATGGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTTGATTAA
1 AGTAAAAGACTAAAAGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGA-TGA
*
575042 AAGGTTAAATGCCTTTG
65 AAGGTTAAATACCTTTG
* * * *
575059 AGTAAAAGACTAAAAGCCTAGATGTGCATTTGGCAGAAATGTGTCAATCATGCCAGTTAGACGAA
1 AGTAAAAGACTAAAAGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
575124 ACGTTAAAT
66 AGGTTAAAT
575133 GCTCTAGACG
Statistics
Matches: 206, Mismatches: 28, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
79 37 0.18
81 97 0.47
82 72 0.35
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (81 bp):
AGTAAAAGACTAAAAGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
AGGTTAAATACCTTTG
Found at i:575087 original size:163 final size:160
Alignment explanation
Indices: 574817--575132 Score: 407
Period size: 163 Copynumber: 2.0 Consensus size: 160
574807 ACTGTTCTAA
* *
574817 AGTAAAAGACTAAAAGCCTAGCTGCGCATTTGACAAAAAGGTGTATTATCCCAGTTAGATGAAAG
1 AGTAAAAGACTAAAAGCCTAGATGCGCATTTGACAAAAAGGTGTATTATCCCAGTTAGATAAAAG
* ** * * * *
574882 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTGATATAAAGGTGTCAATGAT
66 GTTAAATACCTTTGAGTAAAAGACTAAAAGCCTAGATGTGCATTTGACAGAAAGGTGTCAATCAT
* * *
574947 GTCAGTTAGATGAAAGGTTAAATACCTTTG
131 GCCAGTTAGACGAAACGTTAAATACCTTTG
* ** * * * *
574977 AGTAAAAGATTAATGGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTTGATTAA
1 AGTAAAAGACTAAAAGCCTAGATGCGCATTTGACAAAAAGGTGT--ATTATCCCAGTTAGA-TAA
* * *
575042 AAGGTTAAATGCCTTTGAGTAAAAGACTAAAAGCCTAGATGTGCATTTGGCAGAAATGTGTCAAT
63 AAGGTTAAATACCTTTGAGTAAAAGACTAAAAGCCTAGATGTGCATTTGACAGAAAGGTGTCAAT
575107 CATGCCAGTTAGACGAAACGTTAAAT
128 CATGCCAGTTAGACGAAACGTTAAAT
575133 GCTCTAGACG
Statistics
Matches: 131, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
160 38 0.29
162 13 0.10
163 80 0.61
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (160 bp):
AGTAAAAGACTAAAAGCCTAGATGCGCATTTGACAAAAAGGTGTATTATCCCAGTTAGATAAAAG
GTTAAATACCTTTGAGTAAAAGACTAAAAGCCTAGATGTGCATTTGACAGAAAGGTGTCAATCAT
GCCAGTTAGACGAAACGTTAAATACCTTTG
Found at i:577015 original size:19 final size:19
Alignment explanation
Indices: 576991--577028 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
576981 AATTCTAAAC
576991 CGGTTAAAATTTGACAAAA
1 CGGTTAAAATTTGACAAAA
577010 CGGTTAAAATTTGACAAAA
1 CGGTTAAAATTTGACAAAA
577029 TCAATTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (19 bp):
CGGTTAAAATTTGACAAAA
Found at i:577038 original size:19 final size:19
Alignment explanation
Indices: 576994--577037 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
576984 TCTAAACCGG
**
576994 TTAAAATTTGACAAAACGG
1 TTAAAATTTGACAAAACAA
577013 TTAAAATTTGACAAAATCAA
1 TTAAAATTTGACAAAA-CAA
577033 TTAAA
1 TTAAA
577038 TATAATAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (19 bp):
TTAAAATTTGACAAAACAA
Found at i:579976 original size:2 final size:2
Alignment explanation
Indices: 579969--579997 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
579959 AAATGAATCG
579969 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
579998 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:580767 original size:108 final size:108
Alignment explanation
Indices: 580611--580975 Score: 326
Period size: 108 Copynumber: 3.3 Consensus size: 108
580601 AATGTTTCCG
* * *
580611 GTAATTAA-CTGATTATGTTATTGTCAAATTTCTAAGGCTCCATCAGCTTAAACTTTGATAACAT
1 GTAATTAACCT-ATTTTGTTATCGTCAGATTTCTAAGGCTCCATCAGCTTAAACTTTGATAACAT
*
580675 TTTAAGTGTTGCCTAATATGTTGATAATAATGATAATAAATTAA
65 TTTAAGTGTTACCTAATATGTTGATAATAATGATAATAAATTAA
* * * *
580719 GTAACTAACCTATTTTGCTATCGTCAGATTTCTAAGACCCCATCAGCTTTAATAATGCGCTACTT
1 GTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCTCCATCAGC-TT-A-AA----CT--TT
* * * * * ** ** *
580784 -ATTACGTTACATAA-TCGCTACCTAATATGTT-ATTATGGTTGATAAT-GTTTCCA
57 GATAACATT--TTAAGT-GTTACCTAATATGTTGATAAT-AATGATAATAAATT-AA
* * * *
580837 GTAATTAATCTGTTATGTTATCGTCAGATTTCCAAGGCTCCATCAGCTTAAACTTTGATAACATT
1 GTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCTCCATCAGCTTAAACTTTGATAACATT
* * * *
580902 TTAGGTGTTACCTAATATGTTGATAATACTAATAACAAATTAA
66 TTAAGTGTTACCTAATATGTTGATAATAATGATAATAAATTAA
580945 GTAATTAACCTATTTTGTTATCGTCAGATTT
1 GTAATTAACCTATTTTGTTATCGTCAGATTT
580976 TCAAAGCTCC
Statistics
Matches: 196, Mismatches: 42, Indels: 38
0.71 0.15 0.14
Matches are distributed among these distances:
108 87 0.44
109 13 0.07
110 7 0.04
111 4 0.02
115 4 0.02
116 7 0.04
117 11 0.06
118 63 0.32
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (108 bp):
GTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCTCCATCAGCTTAAACTTTGATAACATT
TTAAGTGTTACCTAATATGTTGATAATAATGATAATAAATTAA
Found at i:580815 original size:23 final size:24
Alignment explanation
Indices: 580770--580815 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
580760 ATCAGCTTTA
* *
580770 ATAATGCGCTACTTATTACGTTAC
1 ATAATGCGCTACCTAATACGTTAC
*
580794 ATAAT-CGCTACCTAATATGTTA
1 ATAATGCGCTACCTAATACGTTA
580816 TTATGGTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.37
Consensus pattern (24 bp):
ATAATGCGCTACCTAATACGTTAC
Found at i:580876 original size:226 final size:224
Alignment explanation
Indices: 580473--581071 Score: 833
Period size: 226 Copynumber: 2.7 Consensus size: 224
580463 TTTTAGGCGT
* * * ** * *
580473 TAATATTGATAATAAATCAAGTAATTAACCTATTCTGTTATCGTTGGATTTCTAAGGTCTCATCA
1 TAATAATGATAATAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAA-GCCCCATCA
* *
580538 GCTTTAATAATGCGCTACATATTACGTTACAT-ATGTGATACCTAATATGTTATTATGGTTGATA
65 GCTTTAATAATGCGCTACATATTACGTTACATAAT-CGCTACCTAATATGTTATTATGGTTGATA
* * *
580602 ATGTTTCCGGTAATTAACTGATTATGTTATTGTCAAATTTCTAAGGCTCCATCAGCTTAAACTTT
129 ATGTTTCCAGTAATTAACTG-TTATGTTATCGTCAAATTTCCAAGGCTCCATCAGCTTAAACTTT
*
580667 GATAACATTTTAAGTGTTGCCTAATATGTTGA
193 GATAACATTTTAAGTGTTACCTAATATGTTGA
* *
580699 TAATAATGATAATAAATTAAGTAACTAACCTATTTTGCTATCGTCAGATTTCTAAGACCCCATCA
1 TAATAATGATAATAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAG-CCCCATCA
*
580764 GCTTTAATAATGCGCTACTTATTACGTTACATAATCGCTACCTAATATGTTATTATGGTTGATAA
65 GCTTTAATAATGCGCTACATATTACGTTACATAATCGCTACCTAATATGTTATTATGGTTGATAA
*
580829 TGTTTCCAGTAATTAATCTGTTATGTTATCGTCAGATTTCCAAGGCTCCATCAGCTTAAACTTTG
130 TGTTTCCAGTAATTAA-CTGTTATGTTATCGTCAAATTTCCAAGGCTCCATCAGCTTAAACTTTG
*
580894 ATAACATTTTAGGTGTTACCTAATATGTTGA
194 ATAACATTTTAAGTGTTACCTAATATGTTGA
* * * * * **
580925 TAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTTCAAAGCTCCATTT
1 TAATAATGATAATAAATTAAGTAATTAACCTATTTTGTTATCGTCAGA-TTTCTAAGCCCCATCA
* * * * * *
580990 GCTTTAA-AAAGATGCTACATATTACGTTATATAAGCGCTACCTAATATATTATTATGCTTGATA
65 GCTTTAATAATG-CGCTACATATTACGTTACATAATCGCTACCTAATATGTTATTATGGTTGATA
*
581054 ATGTTTCCATTAATTAAC
129 ATGTTTCCAGTAATTAAC
581072 CAGTTATATT
Statistics
Matches: 333, Mismatches: 35, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
225 5 0.02
226 316 0.95
227 12 0.04
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (224 bp):
TAATAATGATAATAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGCCCCATCAG
CTTTAATAATGCGCTACATATTACGTTACATAATCGCTACCTAATATGTTATTATGGTTGATAAT
GTTTCCAGTAATTAACTGTTATGTTATCGTCAAATTTCCAAGGCTCCATCAGCTTAAACTTTGAT
AACATTTTAAGTGTTACCTAATATGTTGA
Found at i:590769 original size:31 final size:31
Alignment explanation
Indices: 590734--590831 Score: 119
Period size: 31 Copynumber: 3.2 Consensus size: 31
590724 CTTAAGGAAG
590734 AAAATATATTATTTGAAGTTAAGATAATAAC
1 AAAATATATTATTTGAAGTTAAGATAATAAC
* * * * *
590765 AAAATGTATT-TTT-AAGTTAATAAAACAAT
1 AAAATATATTATTTGAAGTTAAGATAATAAC
* *
590794 AAAATATATTACTTGATGTTAAGATAATAAC
1 AAAATATATTATTTGAAGTTAAGATAATAAC
590825 AAAATAT
1 AAAATAT
590832 TTTTTAAATT
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
29 21 0.40
30 5 0.09
31 27 0.51
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (31 bp):
AAAATATATTATTTGAAGTTAAGATAATAAC
Found at i:590782 original size:29 final size:29
Alignment explanation
Indices: 590734--590879 Score: 123
Period size: 29 Copynumber: 4.9 Consensus size: 29
590724 CTTAAGGAAG
590734 AAAATATATTATTTGAAGTTAAGATAATAAC
1 AAAATATATT-TTT-AAGTTAAGATAATAAC
* * * * *
590765 AAAATGTATTTTTAAGTTAATAAAACAAT
1 AAAATATATTTTTAAGTTAAGATAATAAC
* *
590794 AAAATATATTACTTGATGTTAAGATAATAAC
1 AAAATATATT--TTTAAGTTAAGATAATAAC
* * * * * *
590825 AAAATAT-TTTTTAAATTGATAAAAGAAT
1 AAAATATATTTTTAAGTTAAGATAATAAC
*
590853 AAAATATATTTTTAAGTTAAAATAATA
1 AAAATATATTTTTAAGTTAAGATAATA
590880 TATATATATA
Statistics
Matches: 87, Mismatches: 25, Indels: 8
0.73 0.21 0.07
Matches are distributed among these distances:
28 18 0.21
29 35 0.40
30 5 0.06
31 29 0.33
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.38
Consensus pattern (29 bp):
AAAATATATTTTTAAGTTAAGATAATAAC
Found at i:590827 original size:60 final size:59
Alignment explanation
Indices: 590734--590879 Score: 197
Period size: 60 Copynumber: 2.5 Consensus size: 59
590724 CTTAAGGAAG
* * *
590734 AAAATATATTATTTGAAGTTAAGATAATAACAAAATGTATTTTTAAGTTAATAAAACAAT
1 AAAATATATTACTTGAAGTTAAGATAATAACAAAATAT-TTTTTAAATTAATAAAACAAT
* * *
590794 AAAATATATTACTTGATGTTAAGATAATAACAAAATATTTTTTAAATTGATAAAAGAAT
1 AAAATATATTACTTGAAGTTAAGATAATAACAAAATATTTTTTAAATTAATAAAACAAT
* *
590853 AAAATATATT--TTTAAGTTAAAATAATA
1 AAAATATATTACTTGAAGTTAAGATAATA
590880 TATATATATA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
57 14 0.18
59 28 0.36
60 35 0.45
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.38
Consensus pattern (59 bp):
AAAATATATTACTTGAAGTTAAGATAATAACAAAATATTTTTTAAATTAATAAAACAAT
Found at i:592240 original size:28 final size:28
Alignment explanation
Indices: 592209--592271 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
592199 GTTAGATATG
* *
592209 AAAATTATTATTTGA-ATTTAAATTAATT
1 AAAA-TATTATTTAATATTTAAATCAATT
* *
592237 AAAATATTTTTTAATATTTGAATCAATT
1 AAAATATTATTTAATATTTAAATCAATT
592265 -AAATATT
1 AAAATATT
592272 TGAATGAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (28 bp):
AAAATATTATTTAATATTTAAATCAATT
Found at i:592271 original size:17 final size:18
Alignment explanation
Indices: 592249--592290 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
592239 AATATTTTTT
592249 AATATTTGAATCAATT-A
1 AATATTTGAATCAATTCA
*
592266 AATATTTGAATGAATTCA
1 AATATTTGAATCAATTCA
592284 AATATTT
1 AATATTT
592291 TAAAAATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (18 bp):
AATATTTGAATCAATTCA
Found at i:593236 original size:45 final size:46
Alignment explanation
Indices: 593172--593279 Score: 139
Period size: 45 Copynumber: 2.4 Consensus size: 46
593162 AGGTGCACTA
* *
593172 AGAGTGCATCGATTCATCAAGTGCATTCGATG-TTTCA-AAATAGCC
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCC
* *
593217 AGAGTGCATCGATGCATCAAATGTATTCGATGTTTTCATAAAATCC
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCC
**
593263 TCAGTGCATCGATGCAT
1 AGAGTGCATCGATGCAT
593280 GGTATGTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
45 29 0.53
46 23 0.42
47 3 0.05
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (46 bp):
AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCC
Found at i:595995 original size:43 final size:43
Alignment explanation
Indices: 595945--596046 Score: 125
Period size: 43 Copynumber: 2.4 Consensus size: 43
595935 AAACCCAACT
* *
595945 GATGCATCGATGCA-TGGCCTTGTGCATCGATGCACATTCAAG
1 GATGCATCGATGCACTGGCATGGTGCATCGATGCACATTCAAG
* * ** *
595987 GCGTGCATCGGTGCACTTTCATGGTGTATCGATGCACATTCAAG
1 G-ATGCATCGATGCACTGGCATGGTGCATCGATGCACATTCAAG
596031 GATGCATCGATGCACT
1 GATGCATCGATGCACT
596047 ATTAGGTGTA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
42 1 0.02
43 24 0.49
44 24 0.49
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (43 bp):
GATGCATCGATGCACTGGCATGGTGCATCGATGCACATTCAAG
Found at i:595996 original size:23 final size:22
Alignment explanation
Indices: 595966--596045 Score: 99
Period size: 22 Copynumber: 3.6 Consensus size: 22
595956 GCATGGCCTT
595966 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
595988 CGTGCATCGGTGCACTTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
596010 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
596032 ATGCATCGATGCAC
1 GTGCATCGATGCAC
596046 TATTAGGTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 15 0.32
22 16 0.34
23 16 0.34
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:596020 original size:44 final size:42
Alignment explanation
Indices: 595970--596064 Score: 138
Period size: 44 Copynumber: 2.2 Consensus size: 42
595960 GGCCTTGTGC
* *
595970 ATCGATGCACATTCAAGGCGTGCATCGGTGCACT-TTCATGGTGT
1 ATCGATGCACATTCAAGG-ATGCATCGATGCACTATT-A-GGTGT
596014 ATCGATGCACATTCAAGGATGCATCGATGCACTATTAGGTGT
1 ATCGATGCACATTCAAGGATGCATCGATGCACTATTAGGTGT
596056 ATCGATGCA
1 ATCGATGCA
596065 TGAAGCACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
42 14 0.29
43 14 0.29
44 20 0.42
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.28
Consensus pattern (42 bp):
ATCGATGCACATTCAAGGATGCATCGATGCACTATTAGGTGT
Found at i:596022 original size:21 final size:20
Alignment explanation
Indices: 595966--596064 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 20
595956 GCATGGCCTT
595966 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTC-A-G
* *
595988 CGTGCATCGGTGCACTTTCATG
1 -GTGCATCGATGCACATTCA-G
*
596010 GTGTATCGATGCACATTCAAG
1 GTGCATCGATGCACATTC-AG
596031 GATGCATCGATGCACTATT-AG
1 G-TGCATCGATGCAC-ATTCAG
*
596052 GTGTATCGATGCA
1 GTGCATCGATGCA
596065 TGAAGCACAA
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
20 11 0.17
21 20 0.31
22 15 0.23
23 19 0.29
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
GTGCATCGATGCACATTCAG
Found at i:597332 original size:65 final size:64
Alignment explanation
Indices: 597178--597343 Score: 180
Period size: 65 Copynumber: 2.6 Consensus size: 64
597168 AAATAGCCAG
* *
597178 AGTGCATCGATTCGTGGA-TGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCT
1 AGTGCATCGATGCATGGATTGGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CT
597242 C
64 C
* * **
597243 AGTGCATTGATGCATGG-TAT-GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-T
1 AGTGCATCGATGCATGGAT-TGGTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCT
597304 C
64 C
*
597305 ATGGTGCATCGATGCATGGATTGGTGCATCGGTGCATCA
1 A--GTGCATCGATGCATGGATTGGTGCATCGATGCATCA
597344 CTTTGATAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 21 0.25
65 57 0.67
66 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (64 bp):
AGTGCATCGATGCATGGATTGGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTC
Found at i:598379 original size:21 final size:21
Alignment explanation
Indices: 598355--598398 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
598345 TCGGAGGAGG
*
598355 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
* *
598376 AGGAGCAGCTCGTGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
598397 AG
1 AG
598399 CTCCCGGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.41, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAGCT
Found at i:603381 original size:25 final size:25
Alignment explanation
Indices: 603338--603391 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
603328 GCATAGATTA
603338 ATTTCTAATTTTTGGTACCCAAATTT
1 ATTTCTAATTTTTGGTACCCAAA-TT
603364 ATTTCTAA-TTTTGGTACCCAAATT
1 ATTTCTAATTTTTGGTACCCAAATT
603388 ATTT
1 ATTT
603392 TGGGTCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 6 0.21
25 14 0.50
26 8 0.29
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (25 bp):
ATTTCTAATTTTTGGTACCCAAATT
Found at i:610344 original size:18 final size:17
Alignment explanation
Indices: 610290--610338 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
610280 TTGGACCCTT
* *
610290 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
610308 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
610326 AGTGCATTCGATG
1 AGTGCA-TCGATG
610339 TTTCAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:610424 original size:65 final size:64
Alignment explanation
Indices: 610310--610435 Score: 173
Period size: 65 Copynumber: 1.9 Consensus size: 64
610300 TGCACTAAGA
* *
610310 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAATA-CCACAGTGCATCGATGCATGGCTG
* * *
610375 GTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAAAT-CCTCAGTGCATGGATGCATG
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAAATACCACAGTGCATCGATGCATG
610436 AAATGCATTC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
65 44 0.81
66 5 0.09
67 5 0.09
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAATACCACAGTGCATCGATGCATGGCTG
Found at i:610557 original size:15 final size:16
Alignment explanation
Indices: 610537--610571 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
610527 ATTTTGGCTC
610537 AAAATACTTTAAGTA-
1 AAAATACTTTAAGTAT
*
610552 AAAATAGTTTAAGTAT
1 AAAATACTTTAAGTAT
610568 AAAA
1 AAAA
610572 CACAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (16 bp):
AAAATACTTTAAGTAT
Found at i:616178 original size:21 final size:21
Alignment explanation
Indices: 616153--616192 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
616143 AAGACTTTAT
616153 TTTCAAAA-TACAAAAATGATA
1 TTTCAAAATTA-AAAAATGATA
616174 TTTCAAAATTAAAAAATGA
1 TTTCAAAATTAAAAAATGA
616193 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
TTTCAAAATTAAAAAATGATA
Found at i:619130 original size:21 final size:21
Alignment explanation
Indices: 619088--619143 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
619078 TGGGGCAGGA
* *
619088 GGAATCGATACCCCTTGAAGG
1 GGAACCGATACCCCCTGAAGG
* *
619109 GGAACCGATTCCCCCTGGA-G
1 GGAACCGATACCCCCTGAAGG
**
619129 GGAATTGATACCCCC
1 GGAACCGATACCCCC
619144 CACGGGGTCT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.18
Consensus pattern (21 bp):
GGAACCGATACCCCCTGAAGG
Found at i:626408 original size:21 final size:21
Alignment explanation
Indices: 626355--626409 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
626345 TAAGTGTACT
*
626355 GAAGTACCACATATATGTTCC
1 GAAGGACCACATATATGTTCC
* **
626376 AAAGGATTACATATATG-TCTC
1 GAAGGACCACATATATGTTC-C
626397 GAAGGACCACATA
1 GAAGGACCACATA
626410 GAACCCTTAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.25
Consensus pattern (21 bp):
GAAGGACCACATATATGTTCC
Found at i:638036 original size:20 final size:20
Alignment explanation
Indices: 638007--638045 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
637997 CATCCACCAC
*
638007 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
638027 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
638046 TATGGGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:640866 original size:40 final size:40
Alignment explanation
Indices: 640818--640969 Score: 189
Period size: 40 Copynumber: 3.8 Consensus size: 40
640808 AAAGTTAGAA
** * * * *
640818 AATAAAATTCATAAGTAAATCACAATATTAACTCTAGAAC
1 AATAAAATTCATAAACAAACCATAATATTAAGTCTAAAAC
* * *
640858 AACAAAATTTATAAACAAACCATAATATTAAGTCTAAAAT
1 AATAAAATTCATAAACAAACCATAATATTAAGTCTAAAAC
640898 AATAAAATTCATAAACAAACCATAATATTAAGTCTAAAAC
1 AATAAAATTCATAAACAAACCATAATATTAAGTCTAAAAC
*
640938 AAATAAAA-TCGATAAACTAACCATAATATTAA
1 -AATAAAATTC-ATAAACAAACCATAATATTAA
640970 AGGGTCAAAT
Statistics
Matches: 97, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
40 70 0.72
41 27 0.28
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.26
Consensus pattern (40 bp):
AATAAAATTCATAAACAAACCATAATATTAAGTCTAAAAC
Found at i:640935 original size:23 final size:23
Alignment explanation
Indices: 640869--640940 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 23
640859 ACAAAATTTA
640869 TAAACAAACCATAATATTAAGTC
1 TAAACAAACCATAATATTAAGTC
* * *
640892 TAAA-ATA--ATAAAATTCA---
1 TAAACAAACCATAATATTAAGTC
640909 TAAACAAACCATAATATTAAGTC
1 TAAACAAACCATAATATTAAGTC
640932 TAAAACAAA
1 T-AAACAAA
640941 TAAAATCGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 13
0.65 0.11 0.24
Matches are distributed among these distances:
17 4 0.11
18 2 0.06
20 16 0.44
22 2 0.06
23 5 0.14
24 7 0.19
ACGTcount: A:0.58, C:0.14, G:0.03, T:0.25
Consensus pattern (23 bp):
TAAACAAACCATAATATTAAGTC
Found at i:644989 original size:25 final size:26
Alignment explanation
Indices: 644939--644993 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
644929 CGATATCATT
*
644939 TTTGTATATTGAAATTTTTTTCGAAC
1 TTTGTATACTGAAATTTTTTTCGAAC
*
644965 TTTGTATACTG-AATTTTTTTTGAAC
1 TTTGTATACTGAAATTTTTTTCGAAC
644990 TTTG
1 TTTG
644994 AAATCATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 17 0.63
26 10 0.37
ACGTcount: A:0.24, C:0.07, G:0.13, T:0.56
Consensus pattern (26 bp):
TTTGTATACTGAAATTTTTTTCGAAC
Found at i:648336 original size:3 final size:3
Alignment explanation
Indices: 648330--648383 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
648320 GTCTTTAATT
648330 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
648376 TAA -AA TAA
1 TAA TAA TAA
648384 AAACGAATGG
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 6 0.12
3 42 0.88
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:648884 original size:42 final size:40
Alignment explanation
Indices: 648798--648890 Score: 114
Period size: 42 Copynumber: 2.3 Consensus size: 40
648788 ATGAATGGCA
* * * * *
648798 CGAAGGACTTATCATCTTGCTCGAATGACTACAGATGACT
1 CGAAGGATTTATCATCATGCTCAAAAGACTACAGATGACC
*
648838 CGAAGGATTTATGCATCATGCTCAAAAGACTTACTGATGACC
1 CGAAGGATTTAT-CATCATGCTCAAAAGAC-TACAGATGACC
648880 CGAAGGATTTA
1 CGAAGGATTTA
648891 CAAATCAAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 11 0.24
41 14 0.31
42 20 0.44
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (40 bp):
CGAAGGATTTATCATCATGCTCAAAAGACTACAGATGACC
Found at i:649360 original size:42 final size:42
Alignment explanation
Indices: 649306--649423 Score: 164
Period size: 42 Copynumber: 2.8 Consensus size: 42
649296 AAGGTCTTAT
* * *
649306 CATCTTGCTCGAAAGGCTTACAGATGACCCGAAGGATTTAAG
1 CATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAA
**
649348 CATCATGCTCGAAAGACTTATTGATGACCCGAAGGATTTAAA
1 CATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAA
* * *
649390 CATCATACTCGAAAGAATTACAGATGGCCCGAAG
1 CATCATGCTCGAAAGACTTACAGATGACCCGAAG
649424 AACATACAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAA
Found at i:652459 original size:14 final size:15
Alignment explanation
Indices: 652440--652475 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
652430 ATTTTTCATC
652440 TTTTTTCTTTT-TATT
1 TTTTTTCTTTTCT-TT
652455 TTTTTTCTTTTCTTT
1 TTTTTTCTTTTCTTT
652470 TTTTTT
1 TTTTTT
652476 TTCGCTGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTCTTTTCTTT
Found at i:654057 original size:18 final size:17
Alignment explanation
Indices: 654034--654072 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
654024 TGATTCAACA
654034 TTTTTTCATCTTTTTTCC
1 TTTTTTCATCTTTTTT-C
**
654052 TTTTTTTTTCTTTTTTC
1 TTTTTTCATCTTTTTTC
654069 TTTT
1 TTTT
654073 CTTTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTCATCTTTTTTC
Found at i:654059 original size:12 final size:11
Alignment explanation
Indices: 654044--654082 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
654034 TTTTTTCATC
*
654044 TTTTTTCCTTT
1 TTTTTTCTTTT
654055 TTTTTTCTTTT
1 TTTTTTCTTTT
654066 TTCTTTTCTTTT
1 TT-TTTTCTTTT
654078 TTTTT
1 TTTTT
654083 CTGCTGCATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:654077 original size:18 final size:18
Alignment explanation
Indices: 654042--654082 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
654032 CATTTTTTCA
654042 TCTTTTTTCCTTTTTTTT
1 TCTTTTTTCCTTTTTTTT
654060 TCTTTTTT-CTTTTCTTTT
1 TCTTTTTTCCTTTT-TTTT
654078 T-TTTT
1 TCTTTT
654083 CTGCTGCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (18 bp):
TCTTTTTTCCTTTTTTTT
Found at i:654572 original size:11 final size:11
Alignment explanation
Indices: 654552--654582 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
654542 AAATCAATCA
654552 TTTT-TTCTTT
1 TTTTCTTCTTT
654562 TTTTCTTCTTT
1 TTTTCTTCTTT
654573 TTTTCTTCTT
1 TTTTCTTCTT
654583 CTTATTTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTTCTTT
Found at i:663567 original size:15 final size:15
Alignment explanation
Indices: 663547--663575 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
663537 CGCATGCTTC
663547 CCCTTTTTCTCTTTT
1 CCCTTTTTCTCTTTT
663562 CCCTTTTTCTCTTT
1 CCCTTTTTCTCTTT
663576 GCAGCAATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (15 bp):
CCCTTTTTCTCTTTT
Found at i:667338 original size:15 final size:15
Alignment explanation
Indices: 667318--667346 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
667308 TCAGAAGTTT
667318 AATGTGCATATTAGG
1 AATGTGCATATTAGG
667333 AATGTGCATATTAG
1 AATGTGCATATTAG
667347 TAGAACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (15 bp):
AATGTGCATATTAGG
Found at i:667728 original size:13 final size:13
Alignment explanation
Indices: 667712--667751 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
667702 ATAAATGCAA
667712 GTCATAAATGTGT
1 GTCATAAATGTGT
*
667725 GTCATAAATGTGC
1 GTCATAAATGTGT
*
667738 GTCATAAATTTGT
1 GTCATAAATGTGT
667751 G
1 G
667752 ACGCACAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.38
Consensus pattern (13 bp):
GTCATAAATGTGT
Found at i:668134 original size:30 final size:30
Alignment explanation
Indices: 668084--668181 Score: 126
Period size: 29 Copynumber: 3.2 Consensus size: 30
668074 ATCAGATTAT
*
668084 TTCACTTTCATTTCATTTCATAGCATGTTTCA
1 TTCAC-TTCATTT-ATTTCATAGCATGTATCA
668116 TTCACTTCATTTATTTCATA-CATGTATCA
1 TTCACTTCATTTATTTCATAGCATGTATCA
* * * *
668145 TTCATTTAATTCATTTCGTAGCATGTATCA
1 TTCACTTCATTTATTTCATAGCATGTATCA
668175 TTCACTT
1 TTCACTT
668182 ATCATAATCT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
29 24 0.41
30 23 0.39
31 7 0.12
32 5 0.08
ACGTcount: A:0.24, C:0.20, G:0.06, T:0.49
Consensus pattern (30 bp):
TTCACTTCATTTATTTCATAGCATGTATCA
Found at i:674438 original size:2 final size:2
Alignment explanation
Indices: 674431--674457 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
674421 TGTTTTACAT
674431 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
674458 CATCCTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:674732 original size:68 final size:68
Alignment explanation
Indices: 674612--674741 Score: 183
Period size: 68 Copynumber: 1.9 Consensus size: 68
674602 ACTCAATGGT
*
674612 ACTTAATCGTTCATCTAACTGGCATAATTGACACCTTTTTGCCAATTTCACAGTTAGGCCTTAAA
1 ACTTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTTCACAGTTAGGCCTTAAA
674677 GAC
66 GAC
* * * *
674680 ACTTAGTCTTTCATCTAGCTGGCAT-ATATGACACCTTTCTGTC-ATTTGCACAGTTAGGCCTT
1 ACTTAATCGTTCATCTAACTGGCATAAT-TGACACCTTTCTGCCAATTT-CACAGTTAGGCCTT
674742 TACATCTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
67 6 0.11
68 49 0.89
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (68 bp):
ACTTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTTCACAGTTAGGCCTTAAA
GAC
Found at i:675178 original size:79 final size:79
Alignment explanation
Indices: 675067--675378 Score: 444
Period size: 79 Copynumber: 3.9 Consensus size: 79
675057 TTTTATGTTA
* * * * ** * * *
675067 ATAATGCACCCATATGCATTTCAACTTTGGCATCATTTCATTCCAATAATGCACCCATATGCATT
1 ATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATT
* **
675132 ATTATGTTATGTTG
66 ATTATTTTATGCCG
675146 ATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATT
1 ATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATT
*
675211 ATTCTTTTATGCCG
66 ATTATTTTATGCCG
* * * *
675225 ATAATTTACCCATATACATATTAGTTAAGGCATCCTTTCATGACATTAATGCACCCATATGCATT
1 ATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATT
675290 ATTATTTTATGCCG
66 ATTATTTTATGCCG
* *
675304 ATAATGTGCTCATATACATATCAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATT
1 ATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATT
*
675369 ATTCTTTTAT
66 ATTATTTTAT
675379 TCATTAGTTT
Statistics
Matches: 208, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 208 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (79 bp):
ATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCATTAATGCACCCATATGCATT
ATTATTTTATGCCG
Found at i:675892 original size:35 final size:35
Alignment explanation
Indices: 675829--675898 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
675819 TTCGTTCAAG
* *
675829 GTGGTATCGATACCTTCCTTAAGGTATCAGTACCC
1 GTGGTATCGATACATTCCTTAAGATATCAGTACCC
* * *
675864 GTGGTATCGATACATTTCTTCATATATCAGTACCC
1 GTGGTATCGATACATTCCTTAAGATATCAGTACCC
675899 TTGGAATGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.34
Consensus pattern (35 bp):
GTGGTATCGATACATTCCTTAAGATATCAGTACCC
Found at i:676998 original size:12 final size:12
Alignment explanation
Indices: 676981--677022 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
676971 ATTAAGGTAC
676981 TACTAATAATAA
1 TACTAATAATAA
676993 TACTAAT-ATAAA
1 TACTAATAAT-AA
677005 TA-TAATAATAA
1 TACTAATAATAA
*
677016 TAATAAT
1 TACTAAT
677023 TGTAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (12 bp):
TACTAATAATAA
Found at i:677226 original size:30 final size:30
Alignment explanation
Indices: 677192--677261 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
677182 TAGCATGTTC
* *
677192 CATTCACTTCATTTATTTCATAACATCTAT
1 CATTCACTTAATTCATTTCATAACATCTAT
* * * *
677222 CATTCATTTAATTCATTTCGTAACCTGTAT
1 CATTCACTTAATTCATTTCATAACATCTAT
677252 CATTCACTTA
1 CATTCACTTA
677262 TCACAATCTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.29, C:0.23, G:0.03, T:0.46
Consensus pattern (30 bp):
CATTCACTTAATTCATTTCATAACATCTAT
Found at i:677310 original size:2 final size:2
Alignment explanation
Indices: 677299--677330 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
677289 TAAAGTATTG
677299 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
677331 CTCAATGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:680698 original size:16 final size:17
Alignment explanation
Indices: 680677--680710 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
680667 CATGAACTTA
*
680677 AAATGAATGAG-AAATT
1 AAATGAATAAGTAAATT
680693 AAATGAATAAGTAAATT
1 AAATGAATAAGTAAATT
680710 A
1 A
680711 GCGTCTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (17 bp):
AAATGAATAAGTAAATT
Found at i:683454 original size:75 final size:74
Alignment explanation
Indices: 683309--683595 Score: 520
Period size: 74 Copynumber: 3.9 Consensus size: 74
683299 TGATGTTACA
* * * *
683309 AGAGAGAGAGAGAGATGCATGTTGAAGATCATAGAGACTAACAGGGTATAAGAAAAAGAAGTGAA
1 AGAGGGAGAGAGATATGCATGTTGAAGATCATGGAGACTAACAGGGTATAAGAAAAAGTAGTGAA
683374 GCATTAGAG
66 GCATTAGAG
*
683383 ACAGGGAGAGAGATATGCATGTTGAAGATCATGGAGACTTAACAGGGTATAAGAAAAAGTAGTGA
1 AGAGGGAGAGAGATATGCATGTTGAAGATCATGGAGAC-TAACAGGGTATAAGAAAAAGTAGTGA
683448 AGCATTAGAG
65 AGCATTAGAG
683458 AGAGGGAGAGAGATATGCATGTTGAAGATCATGGAGACTAACAGGGTATAAGAAAAAGTAGTGAA
1 AGAGGGAGAGAGATATGCATGTTGAAGATCATGGAGACTAACAGGGTATAAGAAAAAGTAGTGAA
683523 GCATTAGAG
66 GCATTAGAG
683532 AGAGGGAGAGAGATATGCATGTTGAAGATCATGGAGACTAACAGGGTATAAGAAAAAGTAGTGA
1 AGAGGGAGAGAGATATGCATGTTGAAGATCATGGAGACTAACAGGGTATAAGAAAAAGTAGTGA
683596 TGTATTTATA
Statistics
Matches: 206, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
74 134 0.65
75 72 0.35
ACGTcount: A:0.43, C:0.07, G:0.32, T:0.18
Consensus pattern (74 bp):
AGAGGGAGAGAGATATGCATGTTGAAGATCATGGAGACTAACAGGGTATAAGAAAAAGTAGTGAA
GCATTAGAG
Found at i:683483 original size:149 final size:148
Alignment explanation
Indices: 683309--683595 Score: 520
Period size: 149 Copynumber: 1.9 Consensus size: 148
683299 TGATGTTACA
683309 AGAGAGAGAGAGAGATGCATGTTGAAGATCATAGAGACTAACAGGGTATAAGAAAAAGAAGTGAA
1 AGAGAGAGAGAGAGATGCATGTTGAAGATCATAGAGACTAACAGGGTATAAGAAAAAGAAGTGAA
683374 GCATTAGAGACAGGGAGAGAGATATGCATGTTGAAGATCATGGAGACTTAACAGGGTATAAGAAA
66 GCATTAGAGACAGGGAGAGAGATATGCATGTTGAAGATCATGGAGAC-TAACAGGGTATAAGAAA
683439 AAGTAGTGAAGCATTAGAG
130 AAGTAGTGAAGCATTAGAG
* * * *
683458 AGAGGGAGAGAGATATGCATGTTGAAGATCATGGAGACTAACAGGGTATAAGAAAAAGTAGTGAA
1 AGAGAGAGAGAGAGATGCATGTTGAAGATCATAGAGACTAACAGGGTATAAGAAAAAGAAGTGAA
*
683523 GCATTAGAGAGAGGGAGAGAGATATGCATGTTGAAGATCATGGAGACTAACAGGGTATAAGAAAA
66 GCATTAGAGACAGGGAGAGAGATATGCATGTTGAAGATCATGGAGACTAACAGGGTATAAGAAAA
683588 AGTAGTGA
131 AGTAGTGA
683596 TGTATTTATA
Statistics
Matches: 133, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
148 26 0.20
149 107 0.80
ACGTcount: A:0.43, C:0.07, G:0.32, T:0.18
Consensus pattern (148 bp):
AGAGAGAGAGAGAGATGCATGTTGAAGATCATAGAGACTAACAGGGTATAAGAAAAAGAAGTGAA
GCATTAGAGACAGGGAGAGAGATATGCATGTTGAAGATCATGGAGACTAACAGGGTATAAGAAAA
AGTAGTGAAGCATTAGAG
Found at i:686550 original size:24 final size:24
Alignment explanation
Indices: 686499--686550 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
686489 AAAGTTGGAA
*
686499 TTGGAAGGATTCAAACTTGGGACT
1 TTGGAAGGATTCAAACTTGGGACG
*
686523 TTGGAAGGATTCAAACTTGGGCCG
1 TTGGAAGGATTCAAACTTGGGACG
686547 TTGG
1 TTGG
686551 GTTGTCAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.13, G:0.33, T:0.29
Consensus pattern (24 bp):
TTGGAAGGATTCAAACTTGGGACG
Found at i:686832 original size:27 final size:26
Alignment explanation
Indices: 686701--686844 Score: 109
Period size: 28 Copynumber: 5.3 Consensus size: 26
686691 ATCCTAAGTC
* *
686701 AAAAATATATTTT-TTATTCAACTTATT
1 AAAAATATTTTTTATTATTTAAC-T-TT
686728 AAAAATATATTTTTA-T-TTTAAC-TT
1 AAAAATAT-TTTTTATTATTTAACTTT
*
686752 AGAAATATATTTTATTCTTATATTAACTTT
1 A-AAA-ATATTTT-TTATTAT-TTAACTTT
686782 AAAAATATTTAATTCTATTA-TTAACTTT
1 AAAAATATTT--TT-TATTATTTAACTTT
*
686810 AAAAATATTTTTTATTATCTTAACTTC
1 AAAAATATTTTTTATTAT-TTAACTTT
*
686837 AAATATAT
1 AAAAATAT
686845 ATATATATAT
Statistics
Matches: 97, Mismatches: 6, Indels: 28
0.74 0.05 0.21
Matches are distributed among these distances:
24 3 0.03
25 11 0.11
26 8 0.08
27 28 0.29
28 30 0.31
29 9 0.09
30 8 0.08
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (26 bp):
AAAAATATTTTTTATTATTTAACTTT
Found at i:686846 original size:2 final size:2
Alignment explanation
Indices: 686839--686876 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
686829 TTAACTTCAA
686839 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
686877 TTTTTATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:686998 original size:29 final size:29
Alignment explanation
Indices: 686915--687091 Score: 114
Period size: 29 Copynumber: 6.0 Consensus size: 29
686905 TATTATTATC
*
686915 TAAAGTTAATAAAATAATAAAATATATTATT
1 TAAA-TTAATAAAAGAATAAAATATATT-TT
* * *** *
686946 TGAAGT--TAAGTTAATAAAAAATATTTT
1 TAAATTAATAAAAGAATAAAATATATTTT
* * *
686973 TAAACTAATAAAAGAAGAAAATATATCTT
1 TAAATTAATAAAAGAATAAAATATATTTT
*
687002 TAAAGTT-ATCATAAGAATAAAATATA-TTT
1 TAAA-TTAAT-AAAAGAATAAAATATATTTT
* *
687031 TAAAGTTAA-AATAAAAATAAAATATATTTAA
1 TAAA-TTAATAA-AAGAATAAAATATATTT-T
*
687062 TAAGTTGAATAAAA-AATAAAATATATTTT
1 TAAATT-AATAAAAGAATAAAATATATTTT
687091 T
1 T
687092 TAAAGTTAGG
Statistics
Matches: 114, Mismatches: 22, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
27 6 0.05
28 17 0.15
29 44 0.39
30 35 0.31
31 10 0.09
32 2 0.02
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (29 bp):
TAAATTAATAAAAGAATAAAATATATTTT
Found at i:687024 original size:30 final size:28
Alignment explanation
Indices: 686915--687099 Score: 121
Period size: 30 Copynumber: 6.3 Consensus size: 28
686905 TATTATTATC
686915 TAAAGTTA-ATAAAATAATAAAATATATTATT
1 TAAAGTTATAT-AAA-AATAAAATATA-T-TT
* *
686946 TGAAGTTA-AGTTAATAA-AAAATAT-TTT
1 TAAAGTTATA--TAAAAATAAAATATATTT
* * *
686973 TAAACTAATA-AAAGAAGAAAATATATCTT
1 TAAAGTTATATAAA-AATAAAATATAT-TT
*
687002 TAAAGTTATCATAAGAATAAAATATATTT
1 TAAAGTTAT-ATAAAAATAAAATATATTT
*
687031 TAAAGTTAAAATAAAAATAAAATATATTT
1 TAAAGTT-ATATAAAAATAAAATATATTT
*
687060 AATAAGTTGA-ATAAAAAATAAAATATATTTTT
1 TA-AAGTT-ATAT-AAAAATAAAATATA--TTT
687092 TAAAGTTA
1 TAAAGTTA
687100 GGATATGAAT
Statistics
Matches: 125, Mismatches: 15, Indels: 29
0.74 0.09 0.17
Matches are distributed among these distances:
25 2 0.02
26 2 0.02
27 14 0.11
28 3 0.02
29 39 0.31
30 41 0.33
31 17 0.14
32 6 0.05
33 1 0.01
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (28 bp):
TAAAGTTATATAAAAATAAAATATATTT
Found at i:689723 original size:13 final size:14
Alignment explanation
Indices: 689700--689729 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
689690 TTCCCATTAT
689700 AGACGTGCATATGA
1 AGACGTGCATATGA
689714 AGAC-TGCATATGA
1 AGACGTGCATATGA
689727 AGA
1 AGA
689730 TTGTCCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AGACGTGCATATGA
Found at i:690002 original size:15 final size:15
Alignment explanation
Indices: 689982--690184 Score: 219
Period size: 15 Copynumber: 13.5 Consensus size: 15
689972 TGAAAAAAAT
689982 ATAAAATACAATAAC
1 ATAAAATACAATAAC
*
689997 ATAAAATACAATAAT
1 ATAAAATACAATAAC
* * *
690012 ACAATATATAATAAC
1 ATAAAATACAATAAC
*
690027 ATAAAATACAATACC
1 ATAAAATACAATAAC
* *
690042 AGAAAATA-ATATAAT
1 ATAAAATACA-ATAAC
690057 ATAAAATACAATAAC
1 ATAAAATACAATAAC
* **
690072 ATGAAATACAATGCC
1 ATAAAATACAATAAC
* *
690087 AGAAAATAAAATAAC
1 ATAAAATACAATAAC
*
690102 ATAAAATACAATACC
1 ATAAAATACAATAAC
* *
690117 AAAAAATACAATAAT
1 ATAAAATACAATAAC
*
690132 ATAAAATATAATAAC
1 ATAAAATACAATAAC
*
690147 ATAAAATACAATATC
1 ATAAAATACAATAAC
**
690162 ATAAAATACAATATT
1 ATAAAATACAATAAC
690177 ATAAAATA
1 ATAAAATA
690185 TGATATCACA
Statistics
Matches: 152, Mismatches: 34, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
14 1 0.01
15 150 0.99
16 1 0.01
ACGTcount: A:0.64, C:0.11, G:0.02, T:0.23
Consensus pattern (15 bp):
ATAAAATACAATAAC
Found at i:692561 original size:102 final size:102
Alignment explanation
Indices: 692450--692634 Score: 244
Period size: 102 Copynumber: 1.8 Consensus size: 102
692440 AGTAGATGAA
* * * *
692450 ATTTTGATGTTGGGGTCAAAGAAGTTAAAATATGAATACATTCCCCTTGAACTCAAAGGAATATT
1 ATTTCGATGTTGAGGCCAAAGAAGTTAAAAGATGAATACATTCCCCTTGAACTCAAAGGAATATT
692515 ATCATATGAGTTTTGAATGAATTGTTGTGTCTATGGC
66 ATCATATGAGTTTTGAATGAATTGTTGTGTCTATGGC
* * * * * ** * *
692552 ATTTCGATGTTGAGGCCAAAGAAGTTGAAAGATGAATGCCTTCCTCTTGGACTTGAATGCATATT
1 ATTTCGATGTTGAGGCCAAAGAAGTTAAAAGATGAATACATTCCCCTTGAACTCAAAGGAATATT
*
692617 ATCATATGGGTTTTGAAT
66 ATCATATGAGTTTTGAAT
692635 AGACTATCGT
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
102 69 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.36
Consensus pattern (102 bp):
ATTTCGATGTTGAGGCCAAAGAAGTTAAAAGATGAATACATTCCCCTTGAACTCAAAGGAATATT
ATCATATGAGTTTTGAATGAATTGTTGTGTCTATGGC
Found at i:692647 original size:102 final size:101
Alignment explanation
Indices: 692444--692667 Score: 243
Period size: 102 Copynumber: 2.2 Consensus size: 101
692434 TTGTTAAGTA
* * *
692444 GATGAAATTTTGATGTTGGGGTCAAAGAAGTTAAAATATGAATACATTCCCCTTGAACTCAAAGG
1 GATGAAA-TTTGATGTTGAGGCCAAAGAAGTTAAAAGATGAATACATTCCCCTTGAACTCAAAGG
* * *
692509 AATATTATCATATGAGTTTTGAATGAATTGTTGTGTC
65 AATATTATCATATGAGTTTTGAATGAACTATCGTGTC
* ** * * * * * ** *
692546 TATGGCATTTCGATGTTGAGGCCAAAGAAGTTGAAAGATGAATGCCTTCCTCTTGGACTTGAATG
1 GATGAAATTT-GATGTTGAGGCCAAAGAAGTTAAAAGATGAATACATTCCCCTTGAACTCAAAGG
* *
692611 CATATTATCATATGGGTTTTGAAT-AGACTATCGTGTC
65 AATATTATCATATGAGTTTTGAATGA-ACTATCGTGTC
692648 GATGAAATTTGATGTTGAGG
1 GATGAAATTTGATGTTGAGG
692668 TTGAAGAAGT
Statistics
Matches: 98, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
101 14 0.14
102 84 0.86
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (101 bp):
GATGAAATTTGATGTTGAGGCCAAAGAAGTTAAAAGATGAATACATTCCCCTTGAACTCAAAGGA
ATATTATCATATGAGTTTTGAATGAACTATCGTGTC
Found at i:693338 original size:38 final size:38
Alignment explanation
Indices: 693282--693362 Score: 119
Period size: 38 Copynumber: 2.1 Consensus size: 38
693272 GATATAAAAA
* *
693282 ATTTGAGAGTTTTAGATTTCAAGAGAATAGA-GTAGAG
1 ATTTTAGAGTTTTAGATTTCAAGAGAATAAAGGTAGAG
*
693319 AGTTTTAGAGTTTTGGATTTCAAGAGAATAAAGGTAGAG
1 A-TTTTAGAGTTTTAGATTTCAAGAGAATAAAGGTAGAG
693358 ATTTT
1 ATTTT
693363 GAAAGTGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
37 1 0.03
38 31 0.79
39 7 0.18
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (38 bp):
ATTTTAGAGTTTTAGATTTCAAGAGAATAAAGGTAGAG
Found at i:693946 original size:188 final size:190
Alignment explanation
Indices: 693459--693956 Score: 508
Period size: 188 Copynumber: 2.6 Consensus size: 190
693449 AAAAAATGAT
* * * * **
693459 ACACTATGAAATGACAAAGATTCTATACAAAATGTGAAAAAGTTTCTTGTGAAAAGCAACAACCC
1 ACACTATGAAATGACAGAGATTCTATGCAAAAGGTGAAAAAG-TTCTTGTGAAAAGCATCTTCCC
* * * * * *
693524 CTTTTTATAGAGATTCTCTGCATGAATCACTCAATTTCATGTACATATAATGTTTCTATATGGGG
65 CTTTTTATAGAGATTCTCTACATTAATCACTCAATTT-ATCTACATATAATGTCTCCATACGGGG
* * * *
693589 AACTATTCATCCCAAATATCTTCATGCTTGATGGGATGAGACATTAGTGTCTCAAACTAATGG
129 AACTATT-ATCCCAAATATCTACACGCTTGATGGGATGAGACACTAGTGTCTCAAACTAATAG
* * ** ** *
693652 ACACTATGACATGATAGAGATTCTCCGCAAAAGGTGAAAGAAGTTCTTGTGAAAATTAT-TTTCC
1 ACACTATGAAATGACAGAGATTCTATGCAAAAGGTGAAA-AAGTTCTTGTGAAAAGCATCTTCCC
* * * * * *
693716 CTTTTTACAAAGATTCTCTCCATTAACCAATTAATTTTATCTACATATAATG-CTCCACTACGGG
65 CTTTTTATAGAGATTCTCTACATTAATCACTCAA-TTTATCTACATATAATGTCTCCA-TACGGG
* * *
693780 GAACTATT-T-CC-ATTATCTACACGCTTGATGGGATGAGATACTAGTGTCTCAAATTAATAG
128 GAACTATTATCCCAAATATCTACACGCTTGATGGGATGAGACACTAGTGTCTCAAACTAATAG
* * * *
693840 ACATTATGAAATGGA-AGAGATTCTTTGCAAAAGGTGAAAAAGCTTCTTGCGAAAAGCGTCTTCC
1 ACACTATGAAAT-GACAGAGATTCTATGCAAAAGGTGAAAAAG-TTCTTGTGAAAAGCATCTTCC
* *
693904 CCTTTTTGTAGAGATTCAT-TACATTAATCACTCAGA-TTATCTACAAATAATGT
64 CCTTTTTATAGAGATTC-TCTACATTAATCACTCA-ATTTATCTACATATAATGT
693957 TCCTCTTTGG
Statistics
Matches: 248, Mismatches: 48, Indels: 22
0.78 0.15 0.07
Matches are distributed among these distances:
187 3 0.01
188 101 0.41
189 32 0.13
190 3 0.01
191 3 0.01
192 55 0.22
193 48 0.19
194 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (190 bp):
ACACTATGAAATGACAGAGATTCTATGCAAAAGGTGAAAAAGTTCTTGTGAAAAGCATCTTCCCC
TTTTTATAGAGATTCTCTACATTAATCACTCAATTTATCTACATATAATGTCTCCATACGGGGAA
CTATTATCCCAAATATCTACACGCTTGATGGGATGAGACACTAGTGTCTCAAACTAATAG
Found at i:704073 original size:17 final size:17
Alignment explanation
Indices: 704051--704090 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
704041 CTTTGGCAAC
704051 AACATTCAAAGTA-GATG
1 AACATTCAAA-TATGATG
704068 AACATTCAAATATGATG
1 AACATTCAAATATGATG
*
704085 CACATT
1 AACATT
704091 GAGATGCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (17 bp):
AACATTCAAATATGATG
Found at i:707595 original size:29 final size:29
Alignment explanation
Indices: 707514--707595 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 29
707504 ATATGAATAA
*
707514 TATGTGAGTATA-TATATATATATATATGT
1 TATGTGCGTATATTATATATAT-TATATGT
*
707543 TATGTGCGTATGTGTATATATATTATATG-
1 TATGTGCGTATAT-TATATATATTATATGT
*
707572 TGTGTGCGTATATTATACTATATT
1 TATGTGCGTATATTATA-TATATT
707596 CTTATATGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 4 0.09
29 27 0.59
30 6 0.13
31 9 0.20
ACGTcount: A:0.30, C:0.04, G:0.17, T:0.49
Consensus pattern (29 bp):
TATGTGCGTATATTATATATATTATATGT
Found at i:719367 original size:20 final size:21
Alignment explanation
Indices: 719342--719392 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
719332 AAAGTTTTGG
*
719342 ATCGATCCCTTCACC-ATATA
1 ATCGATCCCTTCACCAAAATA
* *
719362 ATCGATCCCTTTACCAAAATG
1 ATCGATCCCTTCACCAAAATA
719383 ATCGATCCCT
1 ATCGATCCCT
719393 CGATGAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.29, C:0.33, G:0.08, T:0.29
Consensus pattern (21 bp):
ATCGATCCCTTCACCAAAATA
Found at i:719388 original size:21 final size:21
Alignment explanation
Indices: 719341--719415 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
719331 GAAAGTTTTG
* *
719341 GATCGATCCCTTCACC-ATAT
1 GATCGATCCCTTTACCAAAAT
*
719361 AATCGATCCCTTTACCAAAAT
1 GATCGATCCCTTTACCAAAAT
** ** *
719382 GATCGATCCCTCGATGAAAAG
1 GATCGATCCCTTTACCAAAAT
719403 GATCGATCCCTTT
1 GATCGATCCCTTT
719416 CTTGCAACTG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
20 14 0.33
21 29 0.67
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.28
Consensus pattern (21 bp):
GATCGATCCCTTTACCAAAAT
Found at i:719499 original size:20 final size:20
Alignment explanation
Indices: 719473--719531 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
719463 GAAAGTTTTG
719473 GATCGATCCCTTCACCAAA-
1 GATCGATCCCTTCACCAAAC
*
719492 GAATCGATCCCTACACCAAAC
1 G-ATCGATCCCTTCACCAAAC
* *
719513 GATCGATCTCTTTACCAAA
1 GATCGATCCCTTCACCAAA
719532 AAGATTGATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.34, C:0.34, G:0.10, T:0.22
Consensus pattern (20 bp):
GATCGATCCCTTCACCAAAC
Found at i:719694 original size:2 final size:2
Alignment explanation
Indices: 719683--719807 Score: 243
Period size: 2 Copynumber: 63.0 Consensus size: 2
719673 AGAATTAATA
719683 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
719724 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
719766 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
719808 TGCACAAGGT
Statistics
Matches: 122, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 121 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:720537 original size:30 final size:35
Alignment explanation
Indices: 720475--720538 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 35
720465 AAGGTTAAAA
*
720475 GAAATAAGTTAGAAAATAATATAGAATGTTAGAAT
1 GAAATAAGTTAGAAAATAATAGAGAATGTTAGAAT
720510 GAAATAA-TTA-AAAA-AATAGA-AAT-TTAGAA
1 GAAATAAGTTAGAAAATAATAGAGAATGTTAGAA
720539 CATTAAGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 6 0.21
31 3 0.11
32 5 0.18
33 4 0.14
34 3 0.11
35 7 0.25
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.27
Consensus pattern (35 bp):
GAAATAAGTTAGAAAATAATAGAGAATGTTAGAAT
Found at i:722762 original size:23 final size:25
Alignment explanation
Indices: 722715--722764 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
722705 TTTATTTTTT
*
722715 AAAAAATCCACATAAGAACTAATAA
1 AAAAAATCCACATAAGAAATAATAA
*
722740 AAAAAATTCACATAA-AAAT-ATAA
1 AAAAAATCCACATAAGAAATAATAA
722763 AA
1 AA
722765 TTTAAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 6 0.26
24 3 0.13
25 14 0.61
ACGTcount: A:0.68, C:0.12, G:0.02, T:0.18
Consensus pattern (25 bp):
AAAAAATCCACATAAGAAATAATAA
Found at i:729418 original size:73 final size:73
Alignment explanation
Indices: 729297--729455 Score: 246
Period size: 73 Copynumber: 2.2 Consensus size: 73
729287 CGTACCAGGG
* * *
729297 ATTTGAATAACGGGTATCGTGTTCGTGTAATAGCCGTTTCAGACGGCATCTTTACCGTTATATGA
1 ATTTGAATAGCGGGTATCGTGTTCGTGTAATAACCGTTTCAGACGGCATCTTTACCGTTATATAA
* *
729362 TGACTGCT
66 CGACCGCT
* *
729370 ATTTGAATAGCGGGTATCGTGTTCGTGTAATAACCGTTTCAGATGGCATCTTTACCTTTATATAA
1 ATTTGAATAGCGGGTATCGTGTTCGTGTAATAACCGTTTCAGACGGCATCTTTACCGTTATATAA
729435 CGACCGCT
66 CGACCGCT
*
729443 ATTTCAATAGCGG
1 ATTTGAATAGCGG
729456 ACCACTATTT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 78 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (73 bp):
ATTTGAATAGCGGGTATCGTGTTCGTGTAATAACCGTTTCAGACGGCATCTTTACCGTTATATAA
CGACCGCT
Found at i:746922 original size:56 final size:55
Alignment explanation
Indices: 746752--746927 Score: 171
Period size: 56 Copynumber: 3.2 Consensus size: 55
746742 AGTTAACGAT
* *
746752 TGACACCTCTGTTCAGTTAAAAATGACTGAGCACCTCTGTTCTTCAGTCTAGAAAC
1 TGACACCTCTATT-AGTTAAAAATGACTGAGCACCTCTGTCCTTCAGTCTAGAAAC
* * * * * * * *
746808 TGGCACCTCTGCTTTG-T---AATGATTGAGCACCTCTGTCCTTTAATCGACAAAC
1 TGACACCTCT-ATTAGTTAAAAATGACTGAGCACCTCTGTCCTTCAGTCTAGAAAC
* * * *
746860 TAACACCTCTATATAGTTAAAAATGACTGAGCCCCTCTGTGCTTCAGTCTAGAATC
1 TGACACCTCTAT-TAGTTAAAAATGACTGAGCACCTCTGTCCTTCAGTCTAGAAAC
746916 TGACACCTCTAT
1 TGACACCTCTAT
746928 GCTTTATAAG
Statistics
Matches: 92, Mismatches: 22, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
51 1 0.01
52 39 0.42
53 1 0.01
55 1 0.01
56 48 0.52
57 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.31
Consensus pattern (55 bp):
TGACACCTCTATTAGTTAAAAATGACTGAGCACCTCTGTCCTTCAGTCTAGAAAC
Found at i:746962 original size:25 final size:25
Alignment explanation
Indices: 746934--746995 Score: 124
Period size: 25 Copynumber: 2.5 Consensus size: 25
746924 CTATGCTTTA
746934 TAAGATTGAGCACCCTTATATTTTG
1 TAAGATTGAGCACCCTTATATTTTG
746959 TAAGATTGAGCACCCTTATATTTTG
1 TAAGATTGAGCACCCTTATATTTTG
746984 TAAGATTGAGCA
1 TAAGATTGAGCA
746996 TATTTGTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.37
Consensus pattern (25 bp):
TAAGATTGAGCACCCTTATATTTTG
Found at i:748397 original size:40 final size:39
Alignment explanation
Indices: 748348--748424 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 39
748338 GTTAGTTGAC
* *
748348 TACTTGTATGTTAGATGAATCGACTA-GAGTTAGGGATGGG
1 TACTAGTATGATAGATGAATCGA-TAGGA-TTAGGGATGGG
*
748388 TACTAGTATGATAGATGAATTGATAGGATTAGGGATG
1 TACTAGTATGATAGATGAATCGATAGGATTAGGGATG
748425 AACACGAGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 11 0.33
40 22 0.67
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.32
Consensus pattern (39 bp):
TACTAGTATGATAGATGAATCGATAGGATTAGGGATGGG
Found at i:749322 original size:16 final size:16
Alignment explanation
Indices: 749301--749333 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
749291 GTTCTAGGAT
749301 GGTTATGCGTTCATCA
1 GGTTATGCGTTCATCA
749317 GGTTATGCGTTCATCA
1 GGTTATGCGTTCATCA
749333 G
1 G
749334 TCAATTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.36
Consensus pattern (16 bp):
GGTTATGCGTTCATCA
Found at i:751145 original size:22 final size:23
Alignment explanation
Indices: 751093--751144 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 23
751083 ATAAAAATAT
751093 TAATTATTAAAATATATTGATTAA
1 TAATT-TTAAAATATATTGATTAA
751117 TAATTTTAAAA-ATA-TGA-TAA
1 TAATTTTAAAATATATTGATTAA
751137 TATATTTT
1 TA-ATTTT
751145 TTAGTATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.19
21 8 0.30
22 3 0.11
23 6 0.22
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (23 bp):
TAATTTTAAAATATATTGATTAA
Found at i:751295 original size:24 final size:23
Alignment explanation
Indices: 751236--751316 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 23
751226 TAATACAATT
* *
751236 TATAATATTTATTAAT-TTTAAAA
1 TATAATA-TAATTAATAATTAAAA
*
751259 AATAATATAATTAAATAATTAAAA
1 TATAATATAATT-AATAATTAAAA
* * **
751283 TATATTATTATTAATTTTTAAAA
1 TATAATATAATTAATAATTAAAA
751306 TATAATATAAT
1 TATAATATAAT
751317 ATTCTTATTT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
22 4 0.09
23 27 0.59
24 15 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATAATATAATTAATAATTAAAA
Found at i:751312 original size:28 final size:27
Alignment explanation
Indices: 751281--751374 Score: 79
Period size: 28 Copynumber: 3.4 Consensus size: 27
751271 AAATAATTAA
*
751281 AATATATTATTATTAATTTTTAAAATAT
1 AATATA-TATTCTTAATTTTTAAAATAT
* * *
751309 AATATAATATTCTTATTTTATTATTATTAT
1 AATAT-ATATTCTTAATTT-TTA-AAATAT
751339 AATA-ATATTCTT-A-TTTTAATAATAT
1 AATATATATTCTTAATTTTTAA-AATAT
751364 AATATA-ATTCT
1 AATATATATTCT
751375 CTTTAGAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
25 16 0.30
26 3 0.06
28 23 0.43
29 4 0.07
30 8 0.15
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (27 bp):
AATATATATTCTTAATTTTTAAAATAT
Found at i:751347 original size:17 final size:17
Alignment explanation
Indices: 751327--751363 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
751317 ATTCTTATTT
751327 TATTATTATTATAATAA
1 TATTATTATTATAATAA
* *
751344 TATTCTTATTTTAATAA
1 TATTATTATTATAATAA
751361 TAT
1 TAT
751364 AATATAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTATTATTATAATAA
Found at i:751358 original size:14 final size:14
Alignment explanation
Indices: 751313--751359 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
751303 AAATATAATA
751313 TAATATTCTTATTT
1 TAATATTCTTATTT
* * **
751327 TATTATTATTATAA
1 TAATATTCTTATTT
751341 TAATATTCTTATTT
1 TAATATTCTTATTT
751355 TAATA
1 TAATA
751360 ATATAATATA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (14 bp):
TAATATTCTTATTT
Found at i:751373 original size:25 final size:26
Alignment explanation
Indices: 751298--751374 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 26
751288 TATTATTAAT
751298 TTTTAA-AATATAATATAATATTCTTA
1 TTTTAATAATATAATAT-ATATTCTTA
*
751324 TTTTATTATTATTATAATA-ATATTCTTA
1 TTTTA--A-TAATATAATATATATTCTTA
751352 TTTTAATAATATAATATA-ATTCT
1 TTTTAATAATATAATATATATTCT
751375 CTTTAGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
25 14 0.32
26 7 0.16
28 15 0.34
30 8 0.18
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTTAATAATATAATATATATTCTTA
Found at i:755617 original size:22 final size:22
Alignment explanation
Indices: 755581--755643 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
755571 TGATTGTTGC
*
755581 ATATGA-TGTTATCATGAATAT
1 ATATGATTTTTATCATGAATAT
755602 ATATGATTTTTATCAT-ATATAT
1 ATATGATTTTTATCATGA-ATAT
755624 ATATGATTTTTATCATGAAT
1 ATATGATTTTTATCATGAAT
755644 GTTATTTTGG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
21 7 0.18
22 30 0.79
23 1 0.03
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.49
Consensus pattern (22 bp):
ATATGATTTTTATCATGAATAT
Found at i:756107 original size:44 final size:45
Alignment explanation
Indices: 756016--756124 Score: 184
Period size: 45 Copynumber: 2.4 Consensus size: 45
756006 GGAATATGGT
*
756016 TTATGGAATAATGGAAAGTGTATTGGTAAAAATAAGCTTACGAGC
1 TTATGGAATAATGGTAAGTGTATTGGTAAAAATAAGCTTACGAGC
756061 TTATGGAATAATGGTAAGTGTATTGGT-AAAATAAGCTTACGAGC
1 TTATGGAATAATGGTAAGTGTATTGGTAAAAATAAGCTTACGAGC
*
756105 TTATGGGATAAATGGTAAGT
1 TTATGGAAT-AATGGTAAGT
756125 AAATTGATTA
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
44 25 0.41
45 36 0.59
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.31
Consensus pattern (45 bp):
TTATGGAATAATGGTAAGTGTATTGGTAAAAATAAGCTTACGAGC
Found at i:756529 original size:12 final size:12
Alignment explanation
Indices: 756512--756536 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
756502 TTTTCGGAAA
756512 TTACTGTAGCAG
1 TTACTGTAGCAG
756524 TTACTGTAGCAG
1 TTACTGTAGCAG
756536 T
1 T
756537 GTATCGATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (12 bp):
TTACTGTAGCAG
Found at i:762351 original size:22 final size:21
Alignment explanation
Indices: 762317--762357 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
762307 TGATTATTGC
762317 ATATGTTGTTATCATGAATAT
1 ATATGTTGTTATCATGAATAT
*
762338 ATATGATTTTTATCATGAAT
1 ATATG-TTGTTATCATGAAT
762358 GTTATTTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (21 bp):
ATATGTTGTTATCATGAATAT
Found at i:762728 original size:20 final size:20
Alignment explanation
Indices: 762686--762729 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
762676 TTGTATATTG
* ** *
762686 GGCTATTGTCTATTGTTTGT
1 GGCTATTGTCTATGGAATAT
762706 GGCTATTGTCTATGGAATAT
1 GGCTATTGTCTATGGAATAT
762726 GGCT
1 GGCT
762730 TATGGAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.11, G:0.27, T:0.45
Consensus pattern (20 bp):
GGCTATTGTCTATGGAATAT
Found at i:762820 original size:44 final size:45
Alignment explanation
Indices: 762727--762837 Score: 179
Period size: 45 Copynumber: 2.5 Consensus size: 45
762717 ATGGAATATG
*
762727 GCTTATGGAATAATGGAAAGTGTATTGGTAAAAATAAACTTACGA
1 GCTTATGGAATAATGGTAAGTGTATTGGTAAAAATAAACTTACGA
*
762772 GCTTATGGAATAATGGTAAGTGTATTGGT-AAAATAAGCTTACGA
1 GCTTATGGAATAATGGTAAGTGTATTGGTAAAAATAAACTTACGA
*
762816 GCTTATGGGATAAATGGTAAGT
1 GCTTATGGAAT-AATGGTAAGT
762838 AAATTGATAA
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
44 24 0.39
45 38 0.61
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (45 bp):
GCTTATGGAATAATGGTAAGTGTATTGGTAAAAATAAACTTACGA
Found at i:771851 original size:12 final size:13
Alignment explanation
Indices: 771815--771882 Score: 54
Period size: 15 Copynumber: 5.2 Consensus size: 13
771805 TTAATATTTT
771815 AATAATAATATTA
1 AATAATAATATTA
771828 ACATAAATAATATTA
1 A-AT-AATAATATTA
771843 AATAA-AATATT-
1 AATAATAATATTA
* *
771854 -CTAAT-ATTTTAAA
1 AATAATAATATT--A
771867 AATAATAATATTA
1 AATAATAATATTA
771880 AAT
1 AAT
771883 TATTGAACAT
Statistics
Matches: 43, Mismatches: 4, Indels: 16
0.68 0.06 0.25
Matches are distributed among these distances:
10 7 0.16
12 6 0.14
13 7 0.16
14 8 0.19
15 15 0.35
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
AATAATAATATTA
Done.